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Epitope-specific Antibody Design

As a leading custom service provider in antibody field, Creative Biolabs now offers a range of epitope-specific antibody design services. With our well established epitope-specific antibody design platform, we are confident in providing unique epitope-specific antibodies with high specificity and affinity.

Due to the ability to bind certain molecules with high affinity and specificity, antibodies become potent tools in life sciences research, as well as in diagnostic and therapeutic applications. Generally, it is arduous and sometimes difficult to produce antibodies to target specific epitopes within a protein, especially when these epitopes are not effective antigens. Therefore, Creative Biolabs has established a more rational strategy to antibody design, which is peer-reviewed protein engineering algorithm. It is based on natural mAb backbone conformations and sequences which enable to design human, highly developable and stable epitope-specific mAbs. In general, our novel epitope-specific mAbs design service mainly consists of Antibody Structure Modelling, Antibody-antigen Complex Analysis, Computer-aided Affinity Maturation, Antibody Structure Determination, and Experimental Validation.

Antibody Structure Modelling

Antibody modeling takes advantages of canonical loop conformations to graft large segments from experimentally determined structures. Antibody modeling enables to provide energetic calculations to minimize loops, docking approaches to refine the VL–VH relative orientation, as well as de novo prediction of the elusive complementarity determining region (CDR) H3 loop. Creative Biolabs offers two approaches for antibody modeling: homology modeling and antibody initio (or de novo) modeling.

Epitope-specific Antibody DesignFig 1. Three-dimensional structures of GPI homodimers. Part A and B shows the molecular surfaces, Part C and D shows the cartoon views. (Opuni, K. F. M., 2017)

Antibody-antigen Complex Analysis

The development of a rapid computational approach for precisely predicting the structure of antibody–antigen complexes would be very powerful for the progress of novel high-affinity antibodies. Creative Biolabs offers first-class antibody-antigen complex analysis services which takes advantage of state-of-the-art docking software tools. Importantly, our modeling service takes into consideration the latest scientific knowledge of antibody–antigen interactions and conformational flexibility of the CDR region (especially the H3 loop).

Epitope-specific Antibody DesignFig 2. Cartoon view of the immune complex. A murine GPI dimer is simultaneously decorated with GPI-specific monoclonal antibodies 46H9 and 11H3, exhibiting the molecular dimensions of the antigen-antibody complexes. (Opuni, K. F. M., 2017)

Computer-aided Affinity Maturation

Many different mutagenesis methods have proven useful to improve the affinity of candidate therapeutic antibodies produced by phage display. However, one of the major problems associated with affinity maturation by phage display is that it is impossible to generate all possible (combinations of) CDR residue mutants. Creative Biolabs has developed advanced computer-aided affinity maturation method, which is based on the construction of 3D model of antibody variable domains. Besides, the residues affecting affinity can be projected onto the model, hence facilitating the selection of candidate positions for maturation.

Antibody Structure Determination

Structure determination is a process to solve the three-dimensional atomic coordinates of a molecule or biomolecule by an analytical method. A variety of techniques can be applied to structure determination, such as NMR spectroscopy, X-ray crystallography, electron microscopy and molecular modelling. Creative Biolabs offers a full suite of services to help you solve difficult structures with speed and accuracy. Our scientists use state of the art software, to rapidly solve crystal structures of macromolecules and complexes.

Experimental Validation

In order to be a powerful research tool, antibody must bind as specifically as possible, in other words, it binds the correct epitope and is clearly visible above any background. Antibodies are able to be validated in a variety of functional assays, for example, ELISA, immunocytochemistry (ICC), western blotting, co-immunoprecipitation. Creative Biolabs provides comprehensive experimental antibodies validation services for customer.

With our high quality epitope-specific antibody design service, the experienced scientists here at Creative Biolabs are dedicated to help you develop epitope-specific antibodies. We also provide other various services regarding in silico technology. Please feel free to contact us for more information and a detailed quote.


  1. Opuni, K. F. M., (2017). “In silico Epitope Mapping of Glucose-6-Phosphate Isomerase: A Rheumatoid Arthritis Autoantigen.” J Proteomics Bioinform, 10, 60-72.
  2. Sormanni, P., (2015). “Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.” Proceedings of the National Academy of Sciences, 112(32), 9902-9907.
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